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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataagcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA

Basic information

species Zea mays
transcript GRMZM2G095348_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataag-cttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
||| | |||||  | || | ||  | |||  |         |||| |||| | ||||   ||||||||||    |||| | |||| |||| ||||||||||||||||| |||||||||||||||||||| |||||||||||||||||| | |||| ||||||||| |||||| |||||||||||
gtgtgttttcttgataatactgcctgcttatt--------gtctggtgttgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA

upper sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
----gtgcgctttct--ctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataagcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
    |||    ||||   |  |  | |      |||   ||| |  |  |  ||   | || | ||  || ||  |    ||    |||| | || || |||||| | ||| | || ||||||||||||||||| |||||||||||||| |||||||||   || ||||||||| || |||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaa-tcttgactacttttctgtttatcaattt--tttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataa--gcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
        |   |  | ||||| ||    |  ||   || ||||      | |     ||| ||   | |||  | || |  |||| | || || |||||  ||||| | ||||||||||| |||||||| ||||| |||||||| |||||||||   || ||||||||| || |||| || || 
-------gtaagtggatcaatggtttgcattattcaaaatatctcaatgcagtaatcctgattattttttaactgttttactcagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
----gtgcgctttct--ctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataagcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
    |||    ||||   |  |  | |      |||   ||| || |  |  ||   |||| | ||  || ||  |  | ||    |||| | || || |||||| | ||| | || ||||||||||||||||| |||||||||||||| |||||||||   || ||||| ||| |  |||| || || 
gtaagtgaaacttctgcttggattattcaaagttttaaattgcaataa-tcttgactatttttctgtttatcaatt--gtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 16
gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataagcttg---atacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
  |    | || || |    ||| |   |    |||  |  | | ||   | ||||||   ||           |||   || |||| | || |||||||| ||  | || ||  |||||||||||||||| ||||||||||| || ||||| ||  | || | |||||| ||| |  | || || 
--gtaagtgct-tagatttgtgtgtttatataattgagat-tgttctagaagtttctgatgctgttcccctgttttgtggatgcagTGTTATAGGGTACACCTTGTTGCTAAGCCTGATTGAGTACAAGACTCTTGTGATGCGGGGTGATTTAGACAAAGCCAGTGAAATCTTACCTACAATTCCT

upper sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
------gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgttaatttctgtgactaacatataagcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
          | |||      |  | || |  |  | |||||||||      |  | | ||||||| | |   ||| |      |||||| | ||||| ||||| |||||| | |||||||||||||||||||| |||||||||||||| ||||||||||| || |||||| | ||| | || || || 
gtaagcagatgttttactgttatgattgctaacaatgttttgtaac-----ttactgacttctgtgtccactttatgat-----tacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

upper sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
----gtgcgctttctctaaaac-----aatgtttcctttcttttgtaacatctgc-tgttaatttctgtgactaacatataagcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
    |||  ||||    | ||      | ||     |   | |||||       | | || |||  |  |       |      |  || |||| |||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  ||||||  || |||||| ||||| | || || || 
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC

upper sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 16
gtgcgctttctctaaaacaatgtttcctttcttttgtaacatctgctgtt--aatttctgtga-ctaacatataa-gcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
||| |    ||    | |     |||     | |     | | || | ||  ||||  | | |  | |  |||      | || |||| | || || || || |||||||| | |||||||||||||||||| ||||| |||||||| || ||  ||| ||||| |||||||||| | |  || || 
gtgagggagcttgggagctgcacttctgcaatctgactgcttttgttcttgtaattgatctaaatttatttatgttatcttatgcagTGTTATGGGATATACCTTACTTCTCAATTTGATTGAGTACAAGACACTTGTAATGCGTGGAGACTTTCAACGTGCAAGTGAAATTTTACCTTTGATTCCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 248

GTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAAgtgcgctttc ... cttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 195

GTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAAgtgcgctttc ... cttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 173

GTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAAgtgcgctttc ... cttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

GTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAAgtgcgctttc ... cttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttttgtaacatctgctgttaatttctgtgactaacatataagcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA
                                  taacatataa  TA-rich tract